X3: Albion Prelude

I am having a problem (well, more like a tedious issue) where I have 50 ships in a fleet and they are all identical M3 fighters. However i want to upgrade all of them to have things like Fight Command Software Mk II and Patrol Command Software, however, the stations that hold those upgrades cant hold all 50 fighters at one time. So I cant just run down the list and manually upgrade because only about 10 ships are docked and the rest are in space waiting to dock, and without issuing a new command to the whole wing to undock, I dont know how to cycle which ships are docked and have no control over which ships do dock.

Also, i have tried the "Equip Ships Like" command and selected a ship that I had already upgraded the way i wanted, but none of the other ships upgraded.

if you dock them at a shipyard, you can equip multiple ships at once (small shipyards 4-5 (eg argon prime), large shipyards 10-12 (eg CBSE). Note: ships have to be identical for multiple upgrades to work at shipyards.